HDR= ./Headers
CFLAGS= -O -I$(HDR) -I/opt/local/lib/vni/CTT2.1/include
CC= gcc
LIBS=  -lrans -lstuff -lm -lnghds
LDFLAGS= -L./Lib.linux

TIO= starting.o\
      alloc_geno_pheno.o\
      chk_freq.o chk_geno_pheno.o chk_pheno_drop.o cnt_ph.o\
      force_geno.o\
      infer_pheno.o input_par.o input_loci.o input_ped_pheno.o isort.o\
      look_conf.o looking.o\
      one_scan.o\
      prn_genotype.o prn_inheritance.o prn_nghd.o\
      set_a2g_g2a.o set_fdr_geno_freq.o  set_individual_pheno.o\
      tuning.o tune_conf.o
TIC= $(TIO: .o=.c)
TIO: HDR/start.h 
Starting: $(TIO)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@  $(TIO) $(LIBS)

all:
	make ultraclean
	make libs
	make Starting
	mv Starting ../
	make clean
ultraclean:
	(cd Lib.linux/Rans; make ultraclean)
	(cd Lib.linux/Stuff; make ultraclean)
	(cd Lib.linux/Nghds; make ultraclean)
clean:
	(cd Lib.linux/Rans; make clean)
	(cd Lib.linux/Stuff; make clean)
	(cd Lib.linux/Nghds; make clean)
	\rm *.o
libs:
	(cd Lib.linux/Stuff; make all)
	(cd Lib.linux/Rans; make all)
	(cd Lib.linux/Nghds; make all)






